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Hi ,I'm new to SJARACNe , aftering using downsample to run SJARACNe ,I get consensus_network_ncol_.txt files seperately in TF/SIG，I decided to calculate driver activities with getActivity_individual()…
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Hello, i want to compare between 3 different conditions. do i run pyscenic on each disease and its control only ? or on a subset of the whole object. I noticed the highest RSS is the same TF for th…
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## Section Number
SDPi TF-1 & TF-3
## Priority
- *Medium: Significant issue or clarification. Requires discussion, but should not lead to long debate.*
## Issue
The BICEPS standard prov…
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On today's TF kickoff call, Aaron G brought up an interesting point-- migrating between a server that supports lots of extensions/FEP-specific Activities (with, say, custom properties defined in a sup…
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Hi. Balachander here. I am a visually impaired person working on AI as a data scientist and ML engineer. I am predominantly using Windows for all my development activities as Windows provides a full f…
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Hi, I am running the example of run_viper() but reported an error "Error in as.vector(data) : no method for coercing this S4 class to a vector". Also, when I run run_viper() with my own Seurat objec…
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### **Describe the bug**
When running `decoupler` to infer transcription factor activities using `dc.run_ulm` and pathway activities using `dc.run_mlm`, I encounter an incompatibility issue with `pyp…
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Identify at least 2, ideally 3 alternative methods that can use prior information (known targets of transcription factors) to predict TF activities on single-cell transcriptomic profiles.
These met…
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http://doi.org/10.1371/journal.pcbi.1005403
> Understanding the cell-specific binding patterns of transcription factors (TFs) is fundamental to studying gene regulatory networks in biological syste…
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Hi. I run the pySCENIC CLI and get 3 csv files.
`expr_mat.adjacencies.tsv` from Step 1 `grn`
`regulons.csv` from Step 2 `ctx`
`auc_mtx.csv` from Step 3 `aucell`
After inspecting the regulon…